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⇱ FlyBase Gene Report: Dmel\Spt5

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FB2026_01 , released March 12, 2026
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General Information
Symbol
Dmel\Spt5
Species
D. melanogaster
Name
Spt5
Annotation Symbol
CG7626
Feature Type
FlyBase ID
FBgn0040273
Gene Model Status
Stock Availability
Gene Summary
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF may also promote transcriptional elongation within coding regions. DSIF is required for the transcriptional induction of heat shock response genes and regulation of genes which control anterior-posterior patterning during embryonic development. (UniProt, Q9V460)
Contribute a Gene Snapshot for this gene.
Also Known As

DSIF, dSpt5

Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-89
RefSeq locus
NT_033778 REGION:19437483..19441898
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (18 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from direct assay
enables mRNA binding
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables mRNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000122628
inferred from sequence or structural similarity with UniProtKB:O00267
Biological Process (9 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (8 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with UniProtKB:O00267
inferred from biological aspect of ancestor with PANTHER:PTN000122628
Cellular Component (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of DSIF complex
inferred from sequence or structural similarity with UniProtKB:O00267
inferred from biological aspect of ancestor with PANTHER:PTN000122628
Protein Family (UniProt)
Belongs to the SPT5 family. (Q9V460)
Protein Signatures (InterPro)
Summaries
(Alliance, FBgn0040273 )
Gene Group (FlyBase)
DRB SENSITIVITY-INDUCING FACTOR COMPLEX -
The DRB sensitivity-inducing factor (DSIF) complex is a heterodimer that acts as both a positive and negative transcription elongation factor. DSIF together with negative elongation factor (NELF) complex associates with RNA polymerase II and causes transcriptional pausing. Phosphorylation of DSIF-NELF complexes dissociates NELF from the elongation complex and transforms DSIF into a positive elongation factor. (Adapted from FBrf0235113, FBrf0211126 and FBrf0203142).
Protein Function (UniProtKB)
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF may also promote transcriptional elongation within coding regions. DSIF is required for the transcriptional induction of heat shock response genes and regulation of genes which control anterior-posterior patterning during embryonic development.
(UniProt, Q9V460)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Spt5 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9V460)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.51

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0086531
3460
1078
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0085716
119.4
1078
6.17
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Spt6. Interacts with Spt4 to form DSIF. DSIF interacts with trx, RNA polymerase II and with the FACT complex, which is composed of dre4/Spt16 and Ssrp/Ssrp1. DSIF can also interact with the exosome, a complex with 3'-5' exoribonuclease activity which is composed of at least Csl4, Dis3, Mtr3, Rrp4, Rrp6, Rrp40, Rrp42, Rrp46 and Ski6. DSIF may also interact with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of Cdk9 and cyclin-T (CycT).

(UniProt, Q9V460)
Post Translational Modification

Phosphorylated. Phosphorylation by P-TEFb alleviates transcriptional pausing (By similarity).

Phosphorylation by P-TEFb alleviates transcriptional pausing (PubMed:32966759). Dephosphorylated by the INTAC complex when transcripts are unfavorably configured for transcriptional elongation, leading to premature transcription termination: dephosphorylation is mediated by the mts/PP2A component of the INTAC complex (PubMed:32966759).

(UniProt, Q9V460)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Spt5 using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.44

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Spt5 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
Spt5
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 17 )
For All Classical and Insertion Alleles Show
Other relevant insertions
Transgenic Constructs ( 19 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Spt5
Transgenic constructs containing regulatory region of Spt5
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene partially disrupted in
Inferred from location ( 1 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Mus musculus (laboratory mouse) (1)
Xenopus tropicalis (Western clawed frog) (2)
Danio rerio (Zebrafish) (1)
Caenorhabditis elegans (Nematode, roundworm) (1)
Anopheles gambiae (African malaria mosquito) (1)
Arabidopsis thaliana (thale-cress) (4)
Saccharomyces cerevisiae (Brewer's yeast) (1)
Schizosaccharomyces pombe (Fission yeast) (1)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Spt5. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 0 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 0 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 1 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
Homo sapiens (Human)
Gene name
Score
OMIM
OMIM Phenotype
DO term
Complementation?
Transgene?
13 of 14
Functional Complementation Data
Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
Interactions
Summary of Physical Interactions
Interaction Browsers
Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
Interaction Browsers
Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Interacts with Spt6. Interacts with Spt4 to form DSIF. DSIF interacts with trx, RNA polymerase II and with the FACT complex, which is composed of dre4/Spt16 and Ssrp/Ssrp1. DSIF can also interact with the exosome, a complex with 3'-5' exoribonuclease activity which is composed of at least Csl4, Dis3, Mtr3, Rrp4, Rrp6, Rrp40, Rrp42, Rrp46 and Ski6. DSIF may also interact with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of Cdk9 and cyclin-T (CycT).
(UniProt, Q9V460 )
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
FlyBase
External Links
External Data
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2R
Recombination map
2-89
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
56D5-56D7
Limits computationally determined from genome sequence between P{lacW}htsk06121 and P{lacW}l(2)k00705k00705&P{lacW}mei-W68k05603
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (9)
Genomic Clones (16)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (81)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced
BDGP DGC clones
Other clones
Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)
RNAi and Array Information
Linkouts
DRSC - Results frm RNAi screens
Antibody Information
Laboratory Generated Antibodies
Commercially Available Antibodies
Cell Line Information
Publicly Available Cell Lines
Other Stable Cell Lines

  • New stable cell line derived from OSC : Several stable cell lines were created in OSC cells. The lines are OSC with dPcf11-halo, OSC with Ubi-TurboID-Myc-Panx, OSC with Ubi-TurboID-Myc-Spt5, and OSC with Ubi-TurboID- Myc-YFP.

Other Comments

RNAi screen using dsRNA made from templates generated with primers directed against this gene results in chromosome misalignment on the metaphase spindle when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

The NELF complex (including TH1 and Nelf-E) and DSIF (including Spt5) may cause polymerase to pause in the proximal promoter region of hsp70.

Spt5 may be involved in promoter-associated pausing and transcriptional elongation.

Relationship to Other Genes
Source for database merge of

Source for merge of: Spt5 CG7626

Additional comments
Nomenclature History
Source for database identify of
Nomenclature comments
Etymology
Synonyms and Secondary IDs (9)
Reported As
Symbol Synonym
Spt5
(Hofstetter et al., 2024, Szlanka et al., 2024, Versluis et al., 2024, Dollinger et al., 2023, Erokhin et al., 2023, Escobedo et al., 2023, Gilmour, 2023.5.26, Krasnov et al., 2023, Mazina et al., 2022, Mazina et al., 2021, Rosendo Machado et al., 2021, Huang et al., 2020, Mazina et al., 2020, Mannix et al., 2019, Mazina et al., 2019, Pereira and Paro, 2017, Qiu and Gilmour, 2017, Transgenic RNAi Project members, 2017-, Zhu et al., 2017, Brewer-Jensen et al., 2016, Dorsett, 2016, Li and Gilmour, 2015, Gaertner and Zeitlinger, 2014, Harvey et al., 2013, Jennings, 2013, Kwon et al., 2013, Lagha et al., 2013, Li et al., 2013, Schertel et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Prabhakaran and Kelley, 2012, Fay et al., 2011, Murawska et al., 2011, Gilchrist et al., 2010, Missra and Gilmour, 2010, Ardehali et al., 2009, Chopra et al., 2009, Chopra et al., 2009, Doumanis et al., 2009, Ni et al., 2008, Tsai et al., 2008, Zhou et al., 2008, Goshima et al., 2007, Legube et al., 2006, Mahoney et al., 2006, Papp and Muller, 2006, Breiling et al., 2004)
Name Synonyms
Secondary FlyBase IDs
  • FBgn0034445
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
Study result (0)
Result
Result Type
Title
External Crossreferences and Linkouts ( 66 )
Sequence Crossreferences
NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
Other crossreferences
AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
FlyMine - An integrated database for Drosophila genomics
InterPro - A database of protein families, domains and functional sites
KEGG Genes - Molecular building blocks of life in the genomic space.
MARRVEL_MODEL - MARRVEL (model organism gene)
Linkouts
BioGRID - A database of protein and genetic interactions.
Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
DroID - A comprehensive database of gene and protein interactions.
DRSC - Results frm RNAi screens
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
MIST (protein-protein) - An integrated Molecular Interaction Database
References (113)